ImClone Systems sued its former president and CEO, Sam Waksal, for $26 million yesterday, saying Martha Stewart’s imprisoned cohort never paid income taxes on some of the fortune he made from the company’s stock.

ImClone said that during 1999 and 2001 – years in which Waksal made a killing on biotech stocks – the company never withheld federal, state or city taxes on his stock options, expecting he would do so himself.

But the Delaware-based drug firm said the disgraced tycoon failed to pay a nickel on nearly $63 million in stock compensation received during those years.

In a lawsuit filed yesterday in Manhattan Supreme Court, ImClone said Waksal failed, in addition, to file tax returns for 2000 until February 2003, in anticipation of his sentencing for securities fraud and obstruction of justice.

The company said the IRS had ordered it to cough up for taxes Waksal had failed to pay, and that it had repeatedly asked him to pony up.

According to court documents, Waksal knew or should have known that under federal and state law ImClone would be responsible for his unpaid taxes.

The one-time SoHo playboy pleaded guilty to securities fraud and other charges stemming from his attempt to sell a large block of ImClone stock just before the Food and Drug Administration turned down its application for its experimental cancer drug Erbitux.